We went in March. It's a TERRIBLE time to visit since everyone wants to see the cherry blossoms and there are a million tourists everywhere.
We did Tokyo for 2 days, Kyoto for 2 days, Osaka for a day, and back to Tokyo. We planned too much and it was tiring. Take the bullet train if you're going between cities, so much better than taking a flight.
In Tokyo, we visited the Tsujiki market which was over-crowded for a Monday nut worth the experience, teamLab Planets which was pretty cool but not a must see, the Gundam statue which apparently is gone now. Shinjuku IMO is a must, but prepare for crowds and sensory overload.
In Kyoto, we rented kimonos and took photos at most of the famous temples and the bamboo forest. We stayed at a traditional ryokan - Kyoto Inn Hokkaikan Ohanabo the close to the train station, and the experience was awesome. The owner was so friendly and full of energy. If I ever go back to Kyoto, I would definitely stay there again.
Our 24 hours in Osaka was also really rushed. We went to Dontonburi at night which had a lot of restaurants and shops, also went to Osaka castle to meet with my wife's coworker who she's never seen in person, just on Teams calls. We didn't get to see the inside of Osaka Castle, but the outside was pretty amazing
Overall I loved Japan, and had a fantastic but tiring trip. After you go there, you will be browsing the Bidet Meta Thread and never go back to wiping your ass with toilet paper.